The important human pathogen Bordetella pertussis is the causative agent of whooping cough, which kills hundreds of thousands of babies and children every year. Despite an extensive vaccination regimen, the prevalence of B. pertussis infection has dramatically increased throughout the industrial world in recent years, leading to epidemics in the U.S. and other countries. The reason for the reemergence is unclear but has been proposed to involve ongoing adaptation of the pathogen to an increasingly vaccinated and immune human population. Despite increasing research, studies on the evolution of the bacterial pathogen during infection are missing, hampering efforts to develop new vaccines and treatments. Specifically, there are no analyses of genetic changes that accumulate across the entire bacterial genome during an infection to evaluate the impact of vaccination on the genomic evolution of B. pertussis. In this proposal, we identify sequence changes that arise in B. pertussis genomes during infection which allows direct measurement of the mutation and recombination rates and to gain unprecedented insight into the in vivo evolution of this important human pathogen. We compare pertussis genome evolution in immunologically nave and vaccinated animal hosts, which enables us to elucidate whether the recent resurgence of pertussis disease is associated with vaccine driven evolution of this pathogen.